Protocol

Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of loss-of-function (LOF) versus functional or intermediate (FUNC, INT) variants in the BRCA1 splice region SNVs stratum, AUROC and AUPRC.

15 evaluations · 30 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

15 recorded evaluations, 30 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

15 evaluations · 30 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; BRCA1 splice region SNVs) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUPRC (zero-shot; BRCA1 splice region SNVs)	AUROC (zero-shot; BRCA1 splice region SNVs)
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.919 (best in column)	0.954
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.918	0.959 (best in column)
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.902	0.943
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.901	0.947
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.897	0.942
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.856	0.89
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.847	0.888
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.845	0.887
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.832	0.891
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.784	0.873
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.779	0.861
NT (Evo 2 paper variant effect evaluations)Evaluation	0.611	0.634
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.556	0.675
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.428	0.487
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.403	0.462

All 30 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.856 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CADD on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J685, row 685: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.89 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CADD on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I685, row 685: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.403 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 1 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J681, row 681: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.462 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 1 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I681, row 681: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.919 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B base on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J679, row 679: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.954 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B base on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I679, row 679: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.918 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J680, row 680: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.959 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I680, row 680: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.902 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B base on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J677, row 677: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.943 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B base on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I677, row 677: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.897 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J678, row 678: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.942 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I678, row 678: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.832 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPN-MSA on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J683, row 683: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.891 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPN-MSA on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I683, row 683: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.611 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J682, row 682: Model 'NT', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.634 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I682, row 682: Model 'NT', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.556 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pangolin on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J691, row 691: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.675 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pangolin on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I691, row 691: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.784 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 100 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J686, row 686: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.873 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 100 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I686, row 686: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.845 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 241 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J687, row 687: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.887 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 241 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I687, row 687: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.847 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 447 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J688, row 688: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.888 AUROC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 447 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I688, row 688: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.779 AUPRC (zero-shot; BRCA1 splice region SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 470 on BRCA1 splice region SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J689, row 689: Model 'PhyloP 470', Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Author-reported evaluations: 15

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3 source records and release history

evo2: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages)
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-brca1-splice-region-snv

areas: dna-genomes
contexts: research
protocol: Score each variant zero-shot (for Evo 2, the log-likelihood of the variant sequence minus that of the reference over an 8,192-bp genomic window around the variant) and compute AUROC and AUPRC for loss-of-function (LOF) versus functional or intermediate (FUNC, INT) variants in the stratum Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA1', Genomic_Feature 'Splice region', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14); Extended Data Fig. 5b
limitations: Positives: 227 loss-of-function (LOF); negatives: 332 functional or intermediate (FUNC, INT); total 559 variants (Supplementary Data 1).; No split: every model scores the same variants zero-shot (SI A.3.12: 'For each benchmark, we score the same variants with all models').; Supervised comparators (AlphaMissense, CADD, SpliceAI, Pangolin) may have been trained on overlapping variants; training overlap is not reported.; No uncertainty is reported.

Related records

part of: Evo 2 paper zero-shot human variant effect evaluations (Brixi et al. 2026)
uses data: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)
assessment: CADD on BRCA1 splice region SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA1 splice region SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA1 splice region SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA1 splice region SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA1 splice region SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA1 splice region SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA1 splice region SNVs (Evo 2 paper)
assessment: NT on BRCA1 splice region SNVs (Evo 2 paper)
assessment: Pangolin on BRCA1 splice region SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA1 splice region SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA1 splice region SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA1 splice region SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA1 splice region SNVs (Evo 2 paper)
assessment: RNA-FM on BRCA1 splice region SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA1 splice region SNVs (Evo 2 paper)

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